But even I think the Calibre UI is pretty awful.
You have software domain knowledge and experience working with spaghetti interfaces assembled by developers rather than designed by experts. You find them more functional because it fits your existing mental model of an interface. However, these interfaces are vastly less functional to everyone else.
An interface that only facilitates beginner workflows is poorly designed. I rarely see these in the wild, but the culprits are usually non-designers pantomiming their understanding of ‘designed’.
I do, however, regularly see developers misinterpret interfaces designed to facilitate advanced functionality for non-developers. Focused views with controls and readouts obscured as appropriate, but functionality exposed through key shortcuts or other means are what most people expect, and it’s a whole lot easier for a developer to learn those usage models than for non-developer users to learn how to use a hundred buttons and readouts acting as a thin wrapper around an API.
The secret probably is having well defined roles: whoever writes the code shouldn't be involved in interface design and vice versa, unless they prove themselves good at it, as the two tasks require very different sets of skills. This is easily accomplished in commercial software writing where roles are defined and salaries paid, but in the FOSS world where everyone and their cat want to be the famous developer, the UI designer role is rarely recognized for its importance.
Calibre's UI isn't illogical or nonsensical, and it can do everything you probably want when it comes to managing an ebook library, converting between book formats, and taking files and off ebook readers. But it doesn't feel like anyone involved with the UI design ever really thought about it from the perspective of "how do I make the common tasks easy" rather than "how do I ensure all the functionality is exposed".
That is, when designing something, and especially when there's nothing to yet dictate what the form should be, let function guide you to it.
If you were to ask "how should a table lamp be designed", I would point to its function -- to give diffuse light and allow switching it on and off -- as the primary guide. Make that work well. Don't let the form get a life of its own that will distract from the function. Rather, the form should serve the function and make it beautiful.